SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_4_S4_L001_R2_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_4_S4_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 713.54 s (45 us/read; 1.32 M reads/minute). === Summary === Total reads processed: 15,706,000 Reads with adapters: 11,248,615 (71.6%) Reads written (passing filters): 15,706,000 (100.0%) Total basepairs processed: 2,355,900,000 bp Quality-trimmed: 9,159,976 bp (0.4%) Total written (filtered): 1,968,243,578 bp (83.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11248615 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 12.2% G: 21.7% T: 36.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2742334 3926500.0 0 2742334 2 376488 981625.0 0 376488 3 202415 245406.2 0 202415 4 115660 61351.6 0 115660 5 96934 15337.9 0 96934 6 82183 3834.5 0 82183 7 66579 958.6 0 66579 8 95001 239.7 0 95001 9 75363 59.9 0 75125 238 10 81209 15.0 1 77351 3858 11 85598 3.7 1 80376 5222 12 86515 0.9 1 81221 5294 13 96527 0.2 1 91069 5458 14 89686 0.2 1 83554 6132 15 72806 0.2 1 68412 4394 16 105343 0.2 1 99018 6325 17 82599 0.2 1 77199 5400 18 79503 0.2 1 74873 4630 19 100299 0.2 1 94044 6255 20 93401 0.2 1 87924 5477 21 81559 0.2 1 76639 4920 22 92216 0.2 1 86910 5306 23 94734 0.2 1 89009 5725 24 95149 0.2 1 89373 5776 25 105782 0.2 1 99776 6006 26 87770 0.2 1 82449 5321 27 95338 0.2 1 88893 6445 28 90298 0.2 1 85892 4406 29 95418 0.2 1 89790 5628 30 93873 0.2 1 89134 4739 31 100963 0.2 1 95205 5758 32 90423 0.2 1 85945 4478 33 99633 0.2 1 93789 5844 34 126170 0.2 1 118899 7271 35 71917 0.2 1 68415 3502 36 98752 0.2 1 93147 5605 37 104121 0.2 1 98203 5918 38 97206 0.2 1 92554 4652 39 94225 0.2 1 89765 4460 40 104186 0.2 1 98424 5762 41 99925 0.2 1 94861 5064 42 102480 0.2 1 97343 5137 43 92586 0.2 1 87878 4708 44 105897 0.2 1 100306 5591 45 112588 0.2 1 106743 5845 46 80544 0.2 1 76510 4034 47 101141 0.2 1 96374 4767 48 98066 0.2 1 93549 4517 49 101791 0.2 1 96776 5015 50 97034 0.2 1 92147 4887 51 120282 0.2 1 114381 5901 52 84235 0.2 1 80401 3834 53 102171 0.2 1 97747 4424 54 76841 0.2 1 73430 3411 55 99264 0.2 1 95032 4232 56 101316 0.2 1 96570 4746 57 94879 0.2 1 90678 4201 58 90444 0.2 1 86700 3744 59 92322 0.2 1 88235 4087 60 94688 0.2 1 90370 4318 61 97150 0.2 1 92685 4465 62 103718 0.2 1 98963 4755 63 136885 0.2 1 131195 5690 64 109397 0.2 1 105405 3992 65 71767 0.2 1 68765 3002 66 78028 0.2 1 74793 3235 67 77090 0.2 1 73810 3280 68 76844 0.2 1 73617 3227 69 75212 0.2 1 71969 3243 70 76863 0.2 1 73510 3353 71 80211 0.2 1 76869 3342 72 75920 0.2 1 72620 3300 73 78093 0.2 1 74948 3145 74 72443 0.2 1 69570 2873 75 68538 0.2 1 65762 2776 76 66619 0.2 1 63921 2698 77 66151 0.2 1 63438 2713 78 62817 0.2 1 60225 2592 79 60312 0.2 1 57778 2534 80 60163 0.2 1 57704 2459 81 57937 0.2 1 55639 2298 82 54845 0.2 1 52637 2208 83 53627 0.2 1 51399 2228 84 50792 0.2 1 48633 2159 85 49633 0.2 1 47523 2110 86 49264 0.2 1 47185 2079 87 49251 0.2 1 47314 1937 88 46501 0.2 1 44723 1778 89 41655 0.2 1 39945 1710 90 39420 0.2 1 37741 1679 91 37399 0.2 1 35859 1540 92 35077 0.2 1 33634 1443 93 32838 0.2 1 31397 1441 94 31873 0.2 1 30582 1291 95 29856 0.2 1 28661 1195 96 27831 0.2 1 26723 1108 97 25609 0.2 1 24584 1025 98 23598 0.2 1 22615 983 99 23296 0.2 1 22392 904 100 21689 0.2 1 20900 789 101 19855 0.2 1 19105 750 102 17867 0.2 1 17193 674 103 15691 0.2 1 15073 618 104 15000 0.2 1 14394 606 105 13326 0.2 1 12799 527 106 12111 0.2 1 11648 463 107 10556 0.2 1 10155 401 108 9460 0.2 1 9085 375 109 8474 0.2 1 8135 339 110 7655 0.2 1 7315 340 111 7041 0.2 1 6747 294 112 6163 0.2 1 5902 261 113 5337 0.2 1 5089 248 114 4565 0.2 1 4367 198 115 3763 0.2 1 3606 157 116 3164 0.2 1 2993 171 117 2789 0.2 1 2653 136 118 2380 0.2 1 2277 103 119 1999 0.2 1 1886 113 120 1562 0.2 1 1470 92 121 1457 0.2 1 1367 90 122 1103 0.2 1 1044 59 123 1029 0.2 1 972 57 124 896 0.2 1 845 51 125 678 0.2 1 637 41 126 611 0.2 1 570 41 127 481 0.2 1 451 30 128 387 0.2 1 354 33 129 379 0.2 1 356 23 130 249 0.2 1 234 15 131 280 0.2 1 263 17 132 196 0.2 1 186 10 133 279 0.2 1 264 15 134 375 0.2 1 361 14 135 138 0.2 1 127 11 136 76 0.2 1 71 5 137 48 0.2 1 43 5 138 41 0.2 1 37 4 139 18 0.2 1 17 1 140 14 0.2 1 12 2 141 8 0.2 1 8 142 12 0.2 1 8 4 143 10 0.2 1 6 4 144 13 0.2 1 11 2 145 15 0.2 1 13 2 146 12 0.2 1 10 2 147 37 0.2 1 35 2 148 25 0.2 1 24 1 149 9 0.2 1 6 3 150 99 0.2 1 92 7 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_4_S4_L001_R2_001.fastq.gz ============================================= 15706000 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 14180 (0.1%)